Searching journal content for articles similar to Zeevi et al. 24 (12): 1991.

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Research: Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging
- Benjamin P. Barré,
- Johan Hallin,
- Jia-Xing Yue,
- Karl Persson,
- Ekaterina Mikhalev,
- Agurtzane Irizar,
- Sylvester Holt,
- Dawn Thompson,
- Mikael Molin,
- Jonas Warringer,
- and Gianni Liti
Genome Res. May 2020 30: 697-710; Published in Advance April 10, 2020, doi:10.1101/gr.253351.119
...with and without treatments promoting life span to provide a detailed portrait of naturally occurring yeast life span variants.ResultsCalorie restriction and rapamycin extend life span through different genetic variantsWe crossed a long-lived North American (NA) oak tree bark strain (YPS128) with a short...
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Research: Core promoter sequence in yeast is a major determinant of expression level
- Shai Lubliner,
- Ifat Regev,
- Maya Lotan-Pompan,
- Sarit Edelheit,
- Adina Weinberger,
- and Eran Segal
Genome Res. July 2015 25: 1008-1017; Published in Advance May 12, 2015, doi:10.1101/gr.188193.114
...in highly active core promoters is focused within a narrow region, that poly(dA:dT) orientation has a functional consequence at the 3′ end of promoters, and that orthologous core promoters across yeast species have conserved activities. Our results demonstrate the importance of core promoters...
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Research: Evolution at two levels of gene expression in yeast
- Carlo G. Artieri and
- Hunter B. Fraser
Genome Res. March 2014 24: 411-421; Published in Advance December 6, 2013, doi:10.1101/gr.165522.113
...explored patterns of sequence divergence in the promoters, 59 UTRs, CDSs, and 39 UTRs among orthologs with reinforcing versus opposing cis-acting divergence and found no significant differences between categories with the exception of slightly increased conservation of the 59 UTRs of opposing orthologs...
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Research: Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast
- C. Joel McManus,
- Gemma E. May,
- Pieter Spealman,
- and Alan Shteyman
Genome Res. March 2014 24: 422-430; Published in Advance December 6, 2013, doi:10.1101/gr.164996.113
.... The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7: 1534–1550. Brem RB, Yvert G, Clinton R, Kruglyak L. 2002. Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752–755. Bullard JH, Mostovoy Y...
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PERSPECTIVE: Changing perspectives in yeast research nearly a decade after the genome sequence
- Kara Dolinski and
- David Botstein
Genome Res. December 2005 15: 1611-1619; doi:10.1101/gr.3727505
...et al. ( 2004 ) identified putative transcription factor binding motifs by using Gibbs sampling to search for significant regulatory elements within promoters of orthologous genes from 13 hemiascomycetous yeasts. Transcription factor binding sites are now also being globally identified via...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...dispersed throughout the The ribosomal-only contigs 19 to 29 (Fig. 2A) display a conserved structural pattern characterized by 45S rDNA genes (18S–5.8S–28S) flanked by a large array of tandemly repeated elements (Fig. 2B,C). We could identify other characteristic motifs: a 160 bp sequence at the 3′ end...
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Research: Transcriptional programs mediating neuronal toxicity and altered glial–neuronal signaling in a Drosophila knock-in tauopathy model
- Hassan Bukhari,
- Vanitha Nithianandam,
- Rachel A. Battaglia,
- Anthony Cicalo,
- Souvarish Sarkar,
- Aram Comjean,
- Yanhui Hu,
- Matthew J. Leventhal,
- Xianjun Dong,
- and Mel B. Feany
Genome Res. April 2024 34: 590-605; Published in Advance April 10, 2024, doi:10.1101/gr.278576.123
...in frontotemporal dementia patients (Poorkaj et al. 2001) and has been frequently modeled in transgenic animals (Goedert and Jakes 2005). The overall structure and expression of TAU are conserved from mammals to Drosophila (Heidary and Fortini 2001), with proline 251 being orthologous to human proline 301. We have...
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Research: Independent evolution of transcript abundance and gene regulatory dynamics
- Gat Krieger,
- Offir Lupo,
- Avraham A. Levy,
- and Naama Barkai
Genome Res. July 2020 30: 1000-1011; Published in Advance July 22, 2020, doi:10.1101/gr.261537.120
...). Examining the promoter of LSO2, we noted that the S. cerevisiae allele has gained a binding site for Sfp1, the principle TF regulating ribosomal protein and ribosomal biogenesis genes (Fig. 7B). Consistent with the differential presence of these binding sites, we find that the S. cerevisiae LSO2 allele...
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Research: Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm
- Shan-Fu Wu,
- Haiying Zhang,
- and Bradley R. Cairns
Genome Res. April 2011 21: 578-589; Published in Advance March 7, 2011, doi:10.1101/gr.113167.110
...the mechanisms underlying the totipotency of vertebrate eggs (Seydoux and Braun 2006), but multiple contributing mechanisms can be envisioned, including maternal RNAs (coding and noncoding) that promote totipotency, the loading and function of key transcription factor proteins (including pluripotency...
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Method: Improved discovery of genetic interactions using CRISPRiSeq across multiple environments
- Mia Jaffe,
- Adam Dziulko,
- Justin D. Smith,
- Robert P. St.Onge,
- Sasha F. Levy,
- and Gavin Sherlock
Genome Res. April 2019 29: 668-681; Published in Advance February 19, 2019, doi:10.1101/gr.246603.118
...under an inducible promoter (Smith et al. 2016; Liu et al. 2017). In yeast, dCas9 fused with the transcriptional repressor Mxi1 has yielded target knockdown levels of up to 53-fold for endogenous targets (Smith et al. 2016; Gilbert et al. 2013). Because gene expression is repressed only after induction...
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